Tim, The thermostat is supposed to be removed from the car during the flush procedure.
The system is definitly supposed to be completely flushed with clean water TWICE after the citric acid treatment and before adding the coolant.
You don't have your year/model listed ... but they specifically suggest AT LEAST 50 percent approved antifreeze .... and I think that is going to be a minimum of 5 liters of actual antifreeze..
They also specifically say that you are not to get below 40 percent.... and if you use only water in the system they have an anticorrosion additive you are supposed to put in....